Index: includes/common.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/common.inc,v
retrieving revision 1.1060
diff -u -p -r1.1060 common.inc
--- includes/common.inc	6 Dec 2009 18:27:23 -0000	1.1060
+++ includes/common.inc	7 Dec 2009 07:59:06 -0000
@@ -5412,6 +5412,7 @@ function drupal_common_theme() {
       'variables' => array('text' => NULL, 'path' => NULL, 'options' => array()),
     ),
     'links' => array(
+      'pattern' => 'links__',
       'variables' => array('links' => NULL, 'attributes' => array('class' => array('links')), 'heading' => array()),
     ),
     'image' => array(
Index: modules/blog/blog.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/blog/blog.module,v
retrieving revision 1.344
diff -u -p -r1.344 blog.module
--- modules/blog/blog.module	4 Dec 2009 16:49:45 -0000	1.344
+++ modules/blog/blog.module	7 Dec 2009 07:59:07 -0000
@@ -86,7 +86,7 @@ function blog_node_view($node, $build_mo
         'attributes' => array('title' => t("Read !username's latest blog entries.", array('!username' => format_username($node)))),
       );
       $node->content['links']['blog'] = array(
-        '#theme' => 'links',
+        '#theme' => array('links__blog_node', 'links'),
         '#links' => $links,
         '#attributes' => array('class' => array('links', 'inline')),
       );
Index: modules/book/book.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/book/book.module,v
retrieving revision 1.529
diff -u -p -r1.529 book.module
--- modules/book/book.module	4 Dec 2009 16:49:45 -0000	1.529
+++ modules/book/book.module	7 Dec 2009 07:59:07 -0000
@@ -113,7 +113,7 @@ function book_node_view_link($node, $bui
 
   if (!empty($links)) {
     $node->content['links']['book'] = array(
-      '#theme' => 'links',
+      '#theme' => array('links__book_node', 'links'),
       '#links' => $links,
       '#attributes' => array('class' => array('links', 'inline')),
     );
Index: modules/comment/comment.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/comment/comment.module,v
retrieving revision 1.814
diff -u -p -r1.814 comment.module
--- modules/comment/comment.module	4 Dec 2009 16:49:46 -0000	1.814
+++ modules/comment/comment.module	7 Dec 2009 07:59:07 -0000
@@ -552,7 +552,7 @@ function comment_node_view($node, $build
     }
 
     $node->content['links']['comment'] = array(
-      '#theme' => 'links',
+      '#theme' => array('links__comment_node', 'links'),
       '#links' => $links,
       '#attributes' => array('class' => array('links', 'inline')),
     );
@@ -840,7 +840,7 @@ function comment_build_content($comment,
 
   if (empty($comment->in_preview)) {
     $comment->content['links']['comment'] = array(
-      '#theme' => 'links',
+      '#theme' => array('links__comment', 'links'),
       '#links' => comment_links($comment, $node),
       '#attributes' => array('class' => array('links', 'inline')),
     );
Index: modules/contextual/contextual.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/contextual/contextual.module,v
retrieving revision 1.1
diff -u -p -r1.1 contextual.module
--- modules/contextual/contextual.module	6 Dec 2009 01:00:27 -0000	1.1
+++ modules/contextual/contextual.module	7 Dec 2009 07:59:07 -0000
@@ -130,7 +130,7 @@ function contextual_links_build($element
     $build = array(
       '#prefix' => '<div class="contextual-links-wrapper">',
       '#suffix' => '</div>',
-      '#theme' => 'links',
+      '#theme' => array('links__contextual', 'links'),
       '#links' => $links,
       '#attributes' => array('class' => array('contextual-links')),
       '#attached' => array(
Index: modules/locale/locale.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/locale/locale.module,v
retrieving revision 1.275
diff -u -p -r1.275 locale.module
--- modules/locale/locale.module	7 Dec 2009 05:02:37 -0000	1.275
+++ modules/locale/locale.module	7 Dec 2009 07:59:08 -0000
@@ -894,7 +894,7 @@ function locale_block_view($type) {
     if (isset($links->links) && count($links->links > 1)) {
       $class = "language-switcher-{$links->provider}";
       $variables = array('links' => $links->links, 'attributes' => array('class' => array($class)));
-      $block['content'] = theme('links', $variables);
+      $block['content'] = theme(array('links__locale_block', 'links'), $variables);
       $block['subject'] = t('Languages');
       return $block;
     }
Index: modules/node/node.admin.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/node/node.admin.inc,v
retrieving revision 1.82
diff -u -p -r1.82 node.admin.inc
--- modules/node/node.admin.inc	4 Dec 2009 16:49:46 -0000	1.82
+++ modules/node/node.admin.inc	7 Dec 2009 07:59:08 -0000
@@ -517,7 +517,7 @@ function node_admin_nodes() {
       // Render an unordered list of operations links.
       $options[$node->nid]['operations'] = array(
         'data' => array(
-          '#theme' => 'links',
+          '#theme' => array('links__node_operations', 'links'),
           '#links' => $operations,
           '#attributes' => array('class' => array('links', 'inline')),
         ),
Index: modules/node/node.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/node/node.module,v
retrieving revision 1.1180
diff -u -p -r1.1180 node.module
--- modules/node/node.module	7 Dec 2009 03:42:27 -0000	1.1180
+++ modules/node/node.module	7 Dec 2009 07:59:08 -0000
@@ -1245,7 +1245,7 @@ function node_build_content($node, $buil
     );
   }
   $node->content['links']['node'] = array(
-    '#theme' => 'links',
+    '#theme' => array('links__node', 'links'),
     '#links' => $links,
     '#attributes' => array('class' => array('links', 'inline')),
   );
Index: modules/poll/poll.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/poll/poll.module,v
retrieving revision 1.328
diff -u -p -r1.328 poll.module
--- modules/poll/poll.module	4 Dec 2009 16:49:47 -0000	1.328
+++ modules/poll/poll.module	7 Dec 2009 07:59:08 -0000
@@ -811,7 +811,7 @@ function theme_poll_choices($variables) 
  * @see theme_poll_results()
  */
 function template_preprocess_poll_results(&$variables) {
-  $variables['links'] = theme('links', array('links' => $variables['raw_links']));
+  $variables['links'] = theme(array('links__poll_results', 'links'), array('links' => $variables['raw_links']));
   if (isset($variables['vote']) && $variables['vote'] > -1 && user_access('cancel own vote')) {
     $variables['cancel_form'] = drupal_render(drupal_get_form('poll_cancel_form', $variables['nid']));
   }
Index: modules/statistics/statistics.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/statistics/statistics.module,v
retrieving revision 1.327
diff -u -p -r1.327 statistics.module
--- modules/statistics/statistics.module	4 Dec 2009 16:49:47 -0000	1.327
+++ modules/statistics/statistics.module	7 Dec 2009 07:59:09 -0000
@@ -117,7 +117,7 @@ function statistics_node_view($node, $bu
     }
 
     $node->content['links']['statistics'] = array(
-      '#theme' => 'links',
+      '#theme' => array('links__statistics_node', 'links'),
       '#links' => $links,
       '#attributes' => array('class' => array('links', 'inline')),
     );
Index: modules/system/page.tpl.php
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/page.tpl.php,v
retrieving revision 1.39
diff -u -p -r1.39 page.tpl.php
--- modules/system/page.tpl.php	20 Nov 2009 04:20:38 -0000	1.39
+++ modules/system/page.tpl.php	7 Dec 2009 07:59:09 -0000
@@ -98,7 +98,7 @@
 
     <?php if ($main_menu): ?>
       <div id="navigation"><div class="section">
-        <?php print theme('links', array('links' => $main_menu, 'attributes' => array('id' => 'main-menu', 'class' => array('links', 'clearfix')), 'heading' => t('Main menu'))); ?>
+        <?php print theme(array('links__system_main_menu', 'links'), array('links' => $main_menu, 'attributes' => array('id' => 'main-menu', 'class' => array('links', 'clearfix')), 'heading' => t('Main menu'))); ?>
       </div></div> <!-- /.section, /#navigation -->
     <?php endif; ?>
 
@@ -136,7 +136,7 @@
     </div></div> <!-- /#main, /#main-wrapper -->
 
     <div id="footer"><div class="section">
-      <?php print theme('links', array('links' => $secondary_menu, 'attributes' => array('id' => 'secondary-menu', 'class' => array('links', 'clearfix')), 'heading' => t('Secondary menu'))); ?>
+      <?php print theme(array('links__system_secondary_menu', 'links'), array('links' => $secondary_menu, 'attributes' => array('id' => 'secondary-menu', 'class' => array('links', 'clearfix')), 'heading' => t('Secondary menu'))); ?>
       <?php print render($page['footer']); ?>
     </div></div> <!-- /.section, /#footer -->
 
Index: modules/toolbar/toolbar.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/toolbar/toolbar.module,v
retrieving revision 1.26
diff -u -p -r1.26 toolbar.module
--- modules/toolbar/toolbar.module	4 Dec 2009 16:49:47 -0000	1.26
+++ modules/toolbar/toolbar.module	7 Dec 2009 07:59:10 -0000
@@ -191,7 +191,7 @@ function toolbar_build() {
   $links = toolbar_menu_navigation_links(toolbar_get_menu_tree());
   $system_menus = menu_list_system_menus();
   $build['toolbar_menu'] = array(
-    '#theme' => 'links',
+    '#theme' => array('links__toolbar_menu', 'links'),
     '#links' => $links,
     '#attributes' => array('id' => 'toolbar-menu'),
     '#heading' => array('text' => t($system_menus['management']), 'level' => 'h2', 'class' => 'element-invisible'),
@@ -220,7 +220,7 @@ function toolbar_build() {
     );
   }
   $build['toolbar_user'] = array(
-    '#theme' => 'links',
+    '#theme' => array('links__toolbar_user', 'links'),
     '#links' => $links,
     '#attributes' => array('id' => 'toolbar-user'),
   );
Index: modules/translation/translation.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/translation/translation.module,v
retrieving revision 1.68
diff -u -p -r1.68 translation.module
--- modules/translation/translation.module	6 Dec 2009 17:56:05 -0000	1.68
+++ modules/translation/translation.module	7 Dec 2009 07:59:10 -0000
@@ -178,7 +178,7 @@ function translation_node_view($node, $b
       // Do not show link to the same node.
       unset($links[$node->language]);
       $node->content['links']['translation'] = array(
-        '#theme' => 'links',
+        '#theme' => array('links__translation_node', 'links'),
         '#links' => $links,
         '#attributes' => array('class' => array('links', 'inline')),
       );
Index: modules/update/update.report.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/update/update.report.inc,v
retrieving revision 1.27
diff -u -p -r1.27 update.report.inc
--- modules/update/update.report.inc	23 Oct 2009 22:24:19 -0000	1.27
+++ modules/update/update.report.inc	7 Dec 2009 07:59:10 -0000
@@ -300,7 +300,7 @@ function theme_update_version($variables
     'title' => t('Release notes'),
     'href' => $version['release_link'],
   );
-  $output .= theme('links', array('links' => $links));
+  $output .= theme(array('links__update_version', 'links'), array('links' => $links));
   $output .= '</td>';
   $output .= '</tr>';
   $output .= "</table>\n";
Index: themes/garland/template.php
===================================================================
RCS file: /cvs/drupal/drupal/themes/garland/template.php,v
retrieving revision 1.35
diff -u -p -r1.35 template.php
--- themes/garland/template.php	1 Dec 2009 15:57:40 -0000	1.35
+++ themes/garland/template.php	7 Dec 2009 07:59:11 -0000
@@ -58,7 +58,7 @@ function garland_process_html(&$vars) {
 function garland_preprocess_page(&$vars) {
   $vars['tabs2'] = menu_secondary_local_tasks();
   if (isset($vars['main_menu'])) {
-    $vars['primary_nav'] = theme('links', array(
+    $vars['primary_nav'] = theme(array('links__system_main_menu', 'links'), array(
       'links' => $vars['main_menu'],
       'attributes' => array(
         'class' => array('links', 'main-menu'),
@@ -74,7 +74,7 @@ function garland_preprocess_page(&$vars)
     $vars['primary_nav'] = FALSE;
   }
   if (isset($vars['secondary_menu'])) {
-    $vars['secondary_nav'] = theme('links', array(
+    $vars['secondary_nav'] = theme(array('links__system_secondary_menu', 'links'), array(
       'links' => $vars['secondary_menu'],
       'attributes' => array(
         'class' => array('links', 'secondary-menu'),